The mammalian gastrointestinal tract is a complex heterogeneous and dynamic environment that hosts a community of symbiotic microbes, the microbiome. The gastrointestinal tract microbiome interacts closely with the host, impacting health, disease and metabolism; changes in its behavior can lead to liver disease, inflammatory/autoimmune disease, transfer of antibiotic resistance, obesity and diabetes, inflammatory bowel disease, pathogenic infections, and cancer. However, there is limited ability to non-destructively and/or non-invasively interrogate the gut. Novel non-destructive or non-invasive strategies are in demand.